Re: [Insight-developers] FEM debian test failures
I spent some time on this too, and again was about to submit a patch
(man, I am just too slow). The code in ComputeMatrix looked a bit odd to
me, ie using where the for counter stopped as a condition in the next
if. I am thinking gcc does some for-loop branching optimization that
does't like this. Anyway, if you compile with the attached patch, the
Spatial Object segfaults go away.
-Paul
On Tue, 2012-06-12 at 13:58 -0400, Bill Lorensen wrote:
> First, I can't imagine how you figured this out. You are starting to
> become a legend in your time...
>
> Why not #ifdef your solution. Something like:
>
> #if (__GNUC__ == 4.7)
> InputVectorType m_MatrixScale __attribute__ ((aligned) );
> #else
> InputVectorType m_MatrixScale;
> #endif
>
>
> On Tue, Jun 12, 2012 at 12:16 PM, Bradley Lowekamp
> <blowekamp@mail.nih.gov> wrote:
> > Hello Steve,
> >
> > I spent some time looking into this.
> >
> > I downloaded the latest Debian 64-bit and then updated to the sid unstable
> > with gcc 4.7. I think this is the same version you are using?
> >
> > These are the failing tests I had:
> >
> > The following tests FAILED:
> > 508 - itkDiffusionTensor3DReconstructionImageFilterTest (SEGFAULT)
> > 885 - itkReadWriteSpatialObjectTest (SEGFAULT)
> > 886 - itkReadWriteSpatialObjectTest1 (SEGFAULT)
> > 887 - itkReadWriteSpatialObjectTest2 (SEGFAULT)
> > 1504 - itkMeshSpatialObjectIOTest (SEGFAULT)
> > 1505 - itkMeshSpatialObjectIOTest1 (SEGFAULT)
> > 1506 - itkMeshSpatialObjectIOTest2 (SEGFAULT)
> > 1924 - itkImageSpatialObjectTest (SEGFAULT)
> > 1925 - itkSpatialObjectToImageStatisticsCalculatorTest (SEGFAULT)
> > 1926 - itkImageMaskSpatialObjectTest (SEGFAULT)
> > 1927 - itkImageMaskSpatialObjectTest2 (SEGFAULT)
> > 1928 - itkImageMaskSpatialObjectTest3 (SEGFAULT)
> > 1931 - itkSceneSpatialObjectTest (SEGFAULT)
> > 1933 - itkMetaArrowConverterTest (SEGFAULT)
> > 1946 - itkArrowSpatialObjectTest (SEGFAULT)
> > 2124 - itkTransformsSetParametersTest (SEGFAULT)
> > Errors while running CTest
> >
> >
> > I was able to repeat many of your test failures. I then hacked and debugged
> > the code for a little bit. I don't see anything wrong with it. Based on you
> > experiment of mixing optimization levels and what I observed, I would tend
> > to agree that there is likely some kind of gcc bug, perhaps in intra-unit
> > optimization or how the data get laid out in certain circumstances.
> >
> > The most interesting things I was able to do it the following change:
> >
> > diff --git a/Modules/Core/Transform/include/itkScalableAffineTransform.h
> > b/Modules/Core/Transform/i
> > index 6032127..8dbcdc4 100644
> > --- a/Modules/Core/Transform/include/itkScalableAffineTransform.h
> > +++ b/Modules/Core/Transform/include/itkScalableAffineTransform.h
> > @@ -166,7 +166,7 @@ private:
> > const Self & operator=(const Self &);
> >
> > double m_Scale[NDimensions];
> > - InputVectorType m_MatrixScale;
> > + InputVectorType m_MatrixScale __attribute__ ((aligned) );
> > }; //class ScalableAffineTransform
> > } // namespace itk
> >
> >
> > With this change all tests pass. Which is _really_ good to know! This mean
> > that all these failing tests are related to this same bug. So I think I have
> > taken this as far as it needs to... I guess I hope that a patch in gcc 4.7
> > will address this issue.
> >
> >
> > On another note. Have you looking at the SimpleITK project? Have you
> > considered also packaging that for Debian distributions?
> >
> > Thanks,
> > Brad
> >
> >
> >
> > On Jun 10, 2012, at 1:41 AM, Steve M. Robbins wrote:
> >
> > On Sun, Jun 10, 2012 at 12:03:39AM -0500, Steve M. Robbins wrote:
> >
> > Well, I spent some time looking at itkReadWriteSpatialObjectTest and
> >
> > I've determined a few things.
> >
> > [...]
> >
> > 2. It works when built using gcc 4.7 in RelWithDebInfo mode (flags -O2 -g).
> >
> > [...]
> >
> > 4. It fails when built using gcc 4.7 with flags -O3 -g -DNDEBUG.
> >
> >
> > One further item. Of the three files that make up
> > ITKIOSpatialObjectsTestDriver, as long as this one
> > is built with -O2:
> >
> > itkPolygonGroupSpatialObjectXMLFileTest.cxx.o
> >
> > I can build the other two with -O3:
> >
> > ITKIOSpatialObjectsTestDriver.cxx.o
> > itkReadWriteSpatialObjectTest.cxx.o
> >
> > and the test completes successfully. This makes no sense to me
> > because itkPolygonGroupSpatialObjectXMLFileTest code is not even
> > executed when running the test in question ("ctest -R
> > itkReadWriteSpatialObjectTest").
> >
> >
> > -Steve
> > <signature.asc>_______________________________________________
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> >
> >
> > ========================================================
> >
> > Bradley Lowekamp
> >
> > Medical Science and Computing for
> >
> > Office of High Performance Computing and Communications
> >
> > National Library of Medicine
> >
> > blowekamp@mail.nih.gov
> >
> >
> >
> >
>
>
>
Description: Fix Spatial Object Test Segfaults
This bug fixes some segfaults that occur when compiling with O3 on gcc
4.7. I am not 100% sure why this works. ComputeMatrix looks fine, just
that it is a bit unusual to use the final counter value of the for loop
as a condition in the next if. I am thinking gcc does some for-loop
branching optimization that does't like this.
Author: Paul Novotny <paul@paulnovo.us>
--- debian-svn.orig/Modules/Core/Transform/include/itkScalableAffineTransform.hxx
+++ debian-svn/Modules/Core/Transform/include/itkScalableAffineTransform.hxx
@@ -180,20 +180,19 @@
ScalableAffineTransform< TScalarType, NDimensions >
::ComputeMatrix()
{
- unsigned int i;
-
- for ( i = 0; i < NDimensions; i++ )
+ bool scaleChanged = false;
+ for ( unsigned int i = 0; i < NDimensions; i++ )
{
if ( m_Scale[i] != m_MatrixScale[i] )
{
- break;
+ scaleChanged = true;
}
}
- if ( i < NDimensions )
+ if ( scaleChanged )
{
MatrixType mat;
typename MatrixType::InternalMatrixType & imat = mat.GetVnlMatrix();
- for ( i = 0; i < NDimensions; i++ )
+ for ( unsigned int i = 0; i < NDimensions; i++ )
{
if ( m_MatrixScale[i] != 0 && m_Scale[i] != 0 )
{
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